rs2061579

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001136262.2(ATXN7L3B):​c.*6069A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,810 control chromosomes in the GnomAD database, including 6,187 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 6187 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

ATXN7L3B
NM_001136262.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.464

Publications

3 publications found
Variant links:
Genes affected
ATXN7L3B (HGNC:37931): (ataxin 7 like 3B) Involved in regulation of gene expression. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATXN7L3BNM_001136262.2 linkc.*6069A>G 3_prime_UTR_variant Exon 1 of 1 ENST00000519948.4 NP_001129734.1 Q96GX2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATXN7L3BENST00000519948.4 linkc.*6069A>G 3_prime_UTR_variant Exon 1 of 1 6 NM_001136262.2 ENSP00000430000.2 Q96GX2

Frequencies

GnomAD3 genomes
AF:
0.260
AC:
39450
AN:
151692
Hom.:
6179
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.438
Gnomad AMI
AF:
0.118
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.264
Gnomad EAS
AF:
0.0918
Gnomad SAS
AF:
0.172
Gnomad FIN
AF:
0.126
Gnomad MID
AF:
0.274
Gnomad NFE
AF:
0.213
Gnomad OTH
AF:
0.250
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
AF:
0.260
AC:
39494
AN:
151810
Hom.:
6187
Cov.:
32
AF XY:
0.253
AC XY:
18754
AN XY:
74208
show subpopulations
African (AFR)
AF:
0.438
AC:
18131
AN:
41408
American (AMR)
AF:
0.174
AC:
2652
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.264
AC:
914
AN:
3462
East Asian (EAS)
AF:
0.0916
AC:
474
AN:
5176
South Asian (SAS)
AF:
0.172
AC:
830
AN:
4822
European-Finnish (FIN)
AF:
0.126
AC:
1340
AN:
10596
Middle Eastern (MID)
AF:
0.284
AC:
83
AN:
292
European-Non Finnish (NFE)
AF:
0.213
AC:
14442
AN:
67770
Other (OTH)
AF:
0.247
AC:
521
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
1323
2646
3970
5293
6616
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
380
760
1140
1520
1900
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.226
Hom.:
2240
Bravo
AF:
0.272
Asia WGS
AF:
0.145
AC:
508
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.60
DANN
Benign
0.22
PhyloP100
-0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2061579; hg19: chr12-74938255; API